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AFAIK DSS2 does a VFR -> CFR conversion, that's why the number of frames changes. DirectShowSource does it only when "convertfps=true" is set.
1.) Try different renderers in MPC and a player without DirectShow like VLC.
2.) Are you sure that the timecodes have been created correctly? Extract them using mkvtoolnix and look at the 30 fps sections.
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